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Theoretical and Computational Chemistry

Working Paper

RASPD+: Fast Protein-Ligand Binding Free Energy Prediction Using Simplified Physicochemical Features

Stefan Holderbach, Lukas Adam, Bhyravabhotla Jayaram, Rebecca Wade, Goutam Mukherjee

Version 2 posted 01 September 2020

875

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Biological and Medicinal Chemistry

Working Paper

Evaluation of Cross-Validation Strategies in Sequence-Based Binding Prediction Using Deep Learning

Angela Lopez-del Rio, Alfons Nonell-Canals, David Vidal, Alexandre Perera-Lluna

Version 1 posted 27 September 2018

646

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Theoretical and Computational Chemistry

Working Paper

Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design

Yuriy Khalak, Gary Tresadern, Matteo Aldeghi, Hannah Magdalena Baumann, David L. Mobley, Bert L. de Groot, Vytautas Gapsys

Version 2 posted 27 September 2021

1,366

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Theoretical and Computational Chemistry

Working Paper

Enhancing Semiempirical Quantum Mechanical Scoring with Machine Learning: a new scoring function that accounts for both the enthalpic and entropic contributions to the ligand binding free energy

Thomas Evangelidis, Ilektra-Chara Giassa,, Mario Lovrić

Version 2 posted 27 December 2022

309

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Biological and Medicinal Chemistry

Working Paper

Long timescale ensemble methods in molecular dynamics: Ligand-protein interactions and allostery in SARS-CoV-2 targets

Agastya P. Bhati, Art Hoti, Andrew Potterton, Mateusz K. Bieniek, Peter V. Coveney

Version 3 posted 10 May 2023

447

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Theoretical and Computational Chemistry

Working Paper

Multi-task Proteochemometric Modelling

Anastasia Pentina, Djork-Arné Clevert

Version 1 posted 16 February 2022

592

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Theoretical and Computational Chemistry

Working Paper

How robust is the ligand binding transition state?

Samik Bose, Samuel Lotz, Indrajit Deb, Megan Shuck, Kin Sing Stephen Lee, Alex Dickson

Version 1 posted 14 August 2023

303

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Theoretical and Computational Chemistry

Working Paper

Large Scale Study of Ligand-Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols

Agastya P Bhati, Peter V. Coveney

Version 2 posted 02 March 2022

502

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Theoretical and Computational Chemistry

Working Paper

Enhancing hit discovery in virtual screening through accurate calculation of absolute protein-ligand binding free energies

Wei Chen, Di Cui, Steven V. Jerome, Mayako Michino, Eelke B. Lenselink, David Huggins, Alexandre Beautrait, Jeremie Vendome, Robert Abel, Richard A. Friesner, Lingle Wang

Version 3 posted 21 December 2022

3,709

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3

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Theoretical and Computational Chemistry

Working Paper

Simulating Protein-Ligand Binding with Neural Network Potentials

Shae-Lynn Lahey, Christopher Rowley

Version 1 posted 29 November 2019

744

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15 results in Protein-Ligand Binding in Keywords: Protein-Ligand Binding

RASPD+: Fast Protein-Ligand Binding Free Energy Prediction Using Simplified Physicochemical Features

Evaluation of Cross-Validation Strategies in Sequence-Based Binding Prediction Using Deep Learning

Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design

Enhancing Semiempirical Quantum Mechanical Scoring with Machine Learning: a new scoring function that accounts for both the enthalpic and entropic contributions to the ligand binding free energy

Long timescale ensemble methods in molecular dynamics: Ligand-protein interactions and allostery in SARS-CoV-2 targets

Multi-task Proteochemometric Modelling

How robust is the ligand binding transition state?

Large Scale Study of Ligand-Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols

Enhancing hit discovery in virtual screening through accurate calculation of absolute protein-ligand binding free energies

Simulating Protein-Ligand Binding with Neural Network Potentials

15 results in Keywords: Protein-Ligand Binding